Go to the folderC:\Users\[User Name]\AppData\Local\Adobe\InDesign\Version [#].0\en_US\Caches\InDesign Recovery and try deleting the recovery files present in the folder.
InDesign checks the InDesign Recovery folder for information on documents that were open when it shut down, and then attempts to open these documents and incorporate any mini-saved data into them.If it will not find anything , it won't ask for any such popups.
NOTE: Only delete the recovery file in case you don't need them in future.